The Clinical Proteomic Tumor Analysis Consortium (CPTAC) will be conducting proteomic analysis of samples that have been previously analyzed by the TCGA. Because of this, there will be a large amount and diversity of data that has already been generated and this will be supplemented with proteomic data from CPTAC. In order to create tools to accommodate the integration of proteomic, genomic and transcriptomic data, the following projects will be initiated: 1) Proteomic-genomic computational analysis tool that will utilize the genomic data to inform searches of the proteomic data for peptides and proteins as well as correlate the genomic data as well as proteomic data both in terms of protein identification and quantification. Once these tools have been developed, the contractor will analyze each tumor dataset that has been subject to analysis in the CPTAC pipeline; 2) Network and pathway analysis tools: these tools will allow the generation of network and pathway data utilizing both the genomic and proteomic data from both CPTAC and TCGA sources. Using these tools, the relationships between genes and proteins will provide the linkage between genes and protein expression in order to provide capabilities using computer modeling to predict such things as the results of pathway perturbations thus providing possible biomarker targets.